PSIFR - a web portal that provides access to TASSER, TASSER-Lite and MetaTASSER and DBD-Hunter, and the enzyme function inference engine EFICaz2.

MetaTASSER - a protein structure prediction server that uses three
state-of-the-art threading methods PROSPECTOR_3, SP3 and SPARKS to identify templates that are selected by 3D-Jury. For targets with no reliable templates, chunk models from chunk-TASSER are also included. SPICKER clustering is used to select the final models from the TASSER trajectory. Detailed atomic models are then built using PULCHRA.

pro-sp3-TASSER - uses a single threading method with multiple scoring to identify templates. Short TASSER runs generate full length models that are selected by TASSER-QA and FTCOM ranking procedures. pro-sp3-TASSER performs better than MetaTASSER for medium/hard targets but is computationally more expensive.

Fr-TM-align - structural alignment program for monomeric proteins that uses the TM-score as the structure comparison metric.

iAlign - structural alignment algorithm for protein-protein interfaces that uses the TM-score as well as a side-chain contact overlap weighted TM-score as the interface comparison metric.

DBD-Threader - a server that predicts DNA-binding protein domains from a protein's sequence.

DBD-Hunter - a server that predicts DNA-binding protein domains given a protein’s structure.

DP-dock - a server that predicts the structure of the DNA/protein complex structure given the tertiary structure of a known DNA-binding protein.

FINDSITE - a threading-based binding site prediction/protein functional inference/ligand screening algorithm that detects common ligand binding sites in a set of evolutionarily related proteins. Crystal structures as well as protein models can be used as the target structures.

BSR - Binding Site Refinement employs a new template-based method for the local refinement of ligand-binding regions in protein models using closely as well as distantly related templates identified by threading.

FINDSITE - a threading-based binding site prediction/protein functional inference/ligand screening algorithm that detects common ligand binding sites in a set of evolutionarily related proteins.

Fr-TM-align - a program for protein structural alignment that uses the TM-score as the structural comparison metric. This is an improved version of Tm-align.

iAlign - a structural alignment algorithm for the protein-protein interface that uses the TM-score as well as a side-chain contact overlap weighted TM-score as the interface comparison metric.

PULCHRA - a program for all-atom reconstruction from the backbone C-alpha atoms.

FINDSITELHM - A homology modeling approach to flexible ligand docking. It uses a collection of common molecule substructures derived from evolutionarily related templates as the reference compounds in similarity-based ligand binding pose prediction.

E. coli Intracellular Dynamics - The inside of cells is highly crowded with bio-macromolecules, such as proteins, DNA, RNA. This environment is quite different from the conditions in a test tube that we usually use for analysis of biomolecular functions, where the macromolecular concentration is ~100 times less than inside cells.

TASSER-VMT-Lite - A light version of the TASSER-VMT method. It builds target-template alignments using SP3 and HHpred methods then builds models using multiple mode of MODELLER. FTCOM is used to select top
models for futher short TASSER refinement. 300 AA protein takes ~ 10 hours.

FINDSITECOMB - Is a tool for large scale virtual ligand screening. It offers the advantage that comparable results are obtained when predicted or experimental structures are used. The user can either provide a protein structure in PDB format or a protein sequence whose structure will first be predicted prior its use in virtual ligand screening.

APoc - Is an efficient tool for large-scale structural comparison of protein pockets for interacting with small-molecule ligands.

IS-score - Is a tool for automatic assessing the quality of protein-protein docking models.

Cavitator - Is a program for detecting "pocket" or "cavity", i.e., potential small-molecule binding sites, in a protein structure.